Goodbye McKay
by thedarklight
Summary: As Atlantis looses an important member of it's team, Elizabeth struggles to come to terms with unrequited feelings.This is a rewrite of the story, thanks to BrownEyes wraithbait for betaing
1. Chapter 1

Part 1: A Dark Day

Summary: Acastus Kolya escapes from the Atlantis Brig, with tragic consequences.

Acastus Kolya was something of a thorn in the expedition's side. The last time the man had been on Atlantis- he'd taken control of the city and nearly killed Rodney and Elizabeth. Then of course there was the incident on Dagan. There was a feeling that it was too good to be true that Kolya was their prisoner; a feeling that was soon to be proven correct. In a perverse twist of fate, Kolya had managed to escape, killing a guard in the process, and was now sneaking up on Dr Rodney McKay.

"Dr McKay, so good to see you again." Kolya said. He was pointing a Beretta at McKay's temple. McKay thought that this had to be some kind of nightmare.

"What do you want?" - McKay asked.

Kolya leaned closer to Rodney and answered, "I would've thought that someone as smart as you could work it out. I want to escape."

"Don't you realise that Colonel Sheppard will never let you leave here alive?"

Kolya grinned at Rodney's remark. "If I escape, I can help the Genii destroy you. If I don't, I will at least know that you die too. So I'm happy either way." Kolya pressed the barrel of the gun against Rodney's temple. Rodney closed his eyes tightly and tried to imagine that this wasn't happening, that he wasn't there and that this maniac wasn't about to kill him.

"Why are you doing this?" Rodney asked.

"Because you are a terrorist and an enemy of the Genii," came the simplistic answer.

Remembering previous experiences, Rodney decided that it wasn't worth arguing with Kolya.

From her position in the control room Elizabeth's jaw dropped in horror when she saw Kolya walking into the gate room. He was holding Rodney in front of him with a gun held up to the side of the terrified scientists head. Closely followed by a security team of marines, John Sheppard rushed into the gate room. However, Kolya was a seasoned soldier who was familiar with tactics. He'd positioned himself close to the gate. They couldn't approach him from behind and from the front there was no clean shot.

"Kolya!" John yelled, taking aim with his P90, "Let him go!"

Kolya chuckled. "Major Sheppard, or should that be Colonel Sheppard, I'm sure that if I let him go then you'll only kill me anyway." he yelled, once again pushing the gun against Rodney's temple. The scientist was already visibly distressed and a few tears were already beginning to form in his eyes. "So lower your weapons or I will kill Dr McKay!"

"_Oh crap! Crap crap crap! I'm going to be killed by this maniac!"_ Was all Rodney could think. He'd been in the field, and had faced death before but he'd never had a gun this close to him before. He was almost paralysed with fear.

"Okay", Sheppard said as he lowered his P90 and gestured with his arms for the Marines to do the same.

"And your side arms," Kolya added. John looked at the Marines and nodded. Then they all removed their side arms and lowered them to the ground. John couldn't work out how things could have gone so badly wrong He expected to wake up and to find that this was all just a bad dream and that his friend would be safe. Kolya slowly walked forward, one arm around Rodney's neck and his other hand pointing the gun to his head.

"I want you to open the Stargate to a Genii-occupied planet!" Kolya ordered.

Elizabeth looked over to a scientist at the control console and nodded. The scientist began punching in the symbols on the DHD and one by one the chevrons lit up. When the wormhole was established, Kolya walked back towards the gate pulling Rodney along with him.

As they neared the event horizon Kolya brought the gun back and ran it down Rodney's apine until it was pressing in-to his lower back. "Time to say goodbye to your friends," Kolya whispered to Rodney. Rodney shivered and John could now see tears running down the Rodney's face. As they were passing the event horizon, Kolya fired.

Rodney felt a sudden shock and for a moment he wasn't sure what was happening. "_I've been shot, that bastard actually shot me!"_ The world seemed to shrink as blackness engulfed him. "_This is it, it's over."_ he thought to himself as he drifted out of thought and conciousness Kolya kept holding on and dragged Rodney's now inert form back through the gate with him, still using him as a human shield, then the gate shut off. An eerie silence filled the room, almost as death itself was in the air. Elizabeth broke down into tears, John felt sick and everyone realised the same thing. They had lost Rodney.


	2. Chapter 2

Part 2: Goodbye Rodney

Summary: The people of Atlantis mourn for Rodney. And some people are feeling especially hurt by events (here is the McWeir stuff)

The news of Rodney's death hit Atlantis like a bomb blast with shock waves reaching every corner of the city. Everyone felt the loss and, although John had lost his best friend, he saw that Elizabeth was suffering the most. After all she had known Rodney since the start of the research program in to the Ancient outpost on Antarctica, and the expedition leader, she felt responsible for the lives of everyone on Atlantis. But there was more to it than that for, in that sickening moment when she saw him die, Elizabeth Weir realised what she had been subconsciously denying all along. She had feelings Rodney McKay, and she would never have the chance to tell him how she felt.

Mechanically, numbly, Elizabeth carried on working. She'd ordered an investigation in-to how Kolya had been able to escape from the brig and after reviewing the surveillance logs and interviewing the key personnel, it had been determined that Kolya had a concealed knife. A knife which had been missed by the personnel who'd searched him. Elizabeth was relieved that there were no traitors in Atlantis, although it was only a small comfort. The guard who had missed the knife had been killed by Kolya in the escape. Elizabeth didn't know what she would have done to him, if he were alive, for getting Rodney killed. The thought chilled her to her core.

She decided that they would hold a memorial service on Rodney's favourite balcony, the one he went to when he wanted to think or just be alone. They tried to limit the service to only his closest friends, although many of the people he worked with tried to attend, but since there wasn't much space, they stood patiently inside whilst the service was held.

It pained her to remember at times that Rodney had said that he never had time for friends but by now those who knew him best could easily see through the acerbic, sarcastic façade he presented. Radek opened the service with a few words about how, even though they were rarely in agreement, he'd respected Dr McKay. When it was John's turn, at first he didn't know what to say.

What could he say? He'd watched his best friend die and there wasn't a single thing he could do about it. Steeling himself against the pain of loss he started to speak and said, "Rodney McKay was a colossal pain in the ass, but he was a good friend who saved my life more times than I can remember." He continued in that vein for a while, probably embellishing the details slightly, but it all seemed appropriate.

Everyone had chance to say goodbye to Rodney in their own way and they left the balcony. That left only the grim task of clearing out his room, his work areas and letting his family know what had happened. Well a cover story for what had happened. Elizabeth knew from the times she had spoken with him in the mess hall that he had a sister, and that his neighbour was looking after Schrödinger, his cat.

Rodney hadn't spoken to his sister for quite a few years and it had been even longer since he had spoken to his parents, so there was probably no way of reaching them. In spite of this, she thought that she should write to them and let them know what had happened.

Elizabeth began to type:

_ i We are sorry to inform you that Dr Rodney McKay was killed in a lab accident. He was an important and popular member of our team... /i _

As she typed she remembered Rodney and she began to sob. It was all too much and everything that had happened that day overwhelmed her. Her head fell in to her arms as she struggled to control the sobs that wracked her body. It wasn't like she'd never had to write condolence letters before. It was that she had never had to write one for somebody so close to her before. Abruptly she sat up and, wiping angrily at her eyes, she pulled her laptop back to her and resumed typing.

When Elizabeth went to sleep that night, she hoped that not only she would not have to live through a day like that again, but also that the look on Rodney's face when he was shot wouldn't haunt her dreams.


	3. Chapter 3

Part 3: The depths of Hell

Summary: Rodney has survived being shot by Kolya, and the Genii have much work for our intrepid scientist.

A groggy Rodney McKay woke up in a poorly-lit, damp room. This didn't seem right, his back hurt and he could smell damp walls and brickwork. This certainly was not Atlantis. He looked down at his stomach to see a rough bandage. He lifted the bandage, ignoring the pain in his torso, exposing recent surgical stitches which didn't seem to be up to Carson's usual standard. Then he remembered the last thing that had happened before he passed out and lay back weakly on the pillow. He had been standing in the gate room, he'd been shot.

Rodney realised the full truth when Acastus Kolya stepped forward out of the shadows and then horror of it hit him full in the guts. "Greetings, Dr McKay," Kolya said grinning down at McKay as he lay helplessly, gaping back at him. "You are now a prisoner of the Genii. You have been brought here because you have skills which may prove useful. But I warn you, if you try to escape, you will be punished and if you cease to be useful, we will have no reason to keep you alive." Kolya seemed to be relishing every word, grinning maliciously at the dazed and bleary scientist.

Although groggy and in pain, Rodney still tried to verbally lash back at Kolya propping himself up on his elbows to do so. "My friends will save me and Sheppard will make you regret the day you were born!" he gasped as forcefully as he could although, because of the state he was in, Rodney's words didn't have quite the effect he had been hoping for.

Kolya laughed menacingly, "Your friends think you are dead! You have no hope of escape, no means of communication and no hope of reaching Atlantis."

Rodney felt the room shrinking and his hands were starting to feel clammy.

"Remember, I once told you that would serve the Genii as punishment for what you've done," and with that Kolya walked out of the room laughing.

Rodney, already in pain from his wound and weak from blood loss and painkillers, fell back onto his bed and finally broke down in tears. He was suffering and he was alone. Rodney could imagine what the Genii wanted. He'd already designed nuclear bombs for them; they probably now wanted delivery systems and more weapons technology.

At that moment he wished that his best friend, John Sheppard was there and that he would be rescued from the depths of Hell. He felt alone now more than ever. He closed his eyes and tried to sleep, welcoming the oblivion.


	4. Chapter 4

Part 4: First Day at Work - A-Bombs and Other Science Fair Projects

Summary: Following his capture by the Genii, Rodney wants to escape but first he has to prove his usefulness to the Genii - his life depends on it.

Rodney spent the next few weeks in the prison hospital either staring at the ceiling or sleeping fitfully. His captors barely spoke to him except to order him about. In spite of his surroundings and the poor medical treatment he was receiving he recovered quickly. He was visited once more by Kolya who looked him up and down and then turned to one of the medics and asked, "Is he ready yet?"

The medic answered, "Yes, you can come for him tomorrow."

Rodney didn't sleep much that night. Although he managed to get a few hours, it didn't seem like sleep, it was more unconsciousness as a result of exhaustion and the drugs he'd been given. Either way, it was interrupted by two guards.

"Report to Chief Cowen," Guard number one informed him. It wasn't a good sign that they weren't even referring to him by name, but they were probably grunts and couldn't even remember it.

"I'm going to need a minute to get dressed," Rodney replied, "and a little privacy." The guards took the not very subtle hint and left the room. He was about to leave the room when he noticed the hole in his shirt. The last few seconds in the gate room came flooding back: he remembered being shot. Rodney walked out of the room determined to escape.

Rodney shifted uncomfortably in his chair. He was sitting in Chief Cowen's office, Cowen was sitting at a desk, Kolya was standing next to Cowen and two guards were standing behind Rodney. Rodney decided that the guards were either there to make sure he wouldn't leave the meeting, or to intimidate him. He couldn't work out why Kolya was there; perhaps he was there just to glare at Rodney.

"You've been brought here because your skills may prove useful to the Genii," Cowen stated. "The C4 provided by Dr Weir has proven useful, but we need more C4 for a number of other projects."

Rodney frowned and said, "Let me guess, you want me to help you make more." He took a deep breath and continued, "Look Cowen, there is no way I can help you. You lack the equipment and the materials. Not to mention the fact that I don't know how to make C4." The familiar snark had returned to Rodney's voice. This wasn't a stalling tactic; Rodney really couldn't help the Genii manufacture a supply of C4.

Cowen scowled. "You don't know? I find that hard to believe."

"Well I'm an astrophysicist, not a chemist. Maybe you should have kidnapped a chemist instead."

"Are you sure about that?"

"Yes," Rodney replied. The expression on Cowen's face didn't fill Rodney with confidence.

"Then in that case, I'm sorry." Cowen nodded to the guards and then looked down to some papers on his desk. The guards walked up to Rodney, each grabbing one of Rodney's arms and pulled him to his feet".

"Take Dr McKay away and have him shot," Cowen said to the guards. He looked up at Rodney, "I'm sorry it had to turn out this way Dr McKay, but you are of no further use."

Rodney started to panic as the guards pulled him towards the door. "Wait, you don't have to do this!" he said, struggling against the guards frantically. He turned to Cowen. "I can help you!" he pleaded. He quickly tried to think about a technology he could help with, after all, he was a genius. "Antibiotics! We traded them in the past, I help you make more."

Cowen shook his head. "Insufficient," he replied.

As Rodney was pulled through the doorway, he yelled, "I can help you strike at the Wraith, without waiting for them to hibernate. I know how to send your weapons up to a hive ship!"

That attracted Cowen's attention. He raised a hand, "Wait." The guards stopped. Cowen got up from his desk and walked up to Rodney. Rodney's gaze met his own. "How?" Cowen asked. He wanted to know if this was just another stalling tactic, or if this he could provide a new tactical advantage.

Rodney sighed and lowered his head slightly. "It's called rocket technology. You can make devices called missiles. They can carry your atomic bombs through the air; they can even reach space if they're powerful enough." Rodney knew he'd regret this; he already gave them one devastating weapon. Now he was about to give them the delivery system. But after going through one near-death experience, he knew that he really didn't want to die.

Cowen smiled and spoke. "That could prove very useful. You're now officially useful again," he said.

Rodney breathed a sigh of relief. Cowen brought his face closer to McKay's. "You'd better be telling the truth, or a firing squad will be the least of your worries," he said threateningly. Then he stepped back and turned to his desk. "Commander Kolya, have a team assigned to Dr McKay. Make sure they have a suitable lab." Kolya nodded and walked away down one of the corridors. Cowen turned back to McKay and said, "It will take some time to set up the facilities. I suggest you get some rest."

Rodney certainly needed to rest, he had thought that he was going to be executed by a bunch of gun-happy Genii soldiers and that could take it out of a guy.

The guards now let go of Rodney's arms and then led him back to his quarters. Once in his quarters, Rodney felt a wave of nausea. He grabbed a bin and threw up, heaving again and again until there was nothing left except a sour taste. He didn't know if this was because he thought he was going to be killed, or if it was because he offered the Genii missile technology. It may have been both.

He noticed that some food had been left on his desk. There was soup, bread and a cup of something which looked like the Pegasus galaxy equivalent of coffee. Rodney hadn't eaten for a few hours. He wondered that was the usual feeding time for prisoners, or if they knew about his hypoglycaemic condition. At least I won't starve and fall into a coma, he thought to himself. Rodney started to eat the soup and bread. He tried the 'coffee' and it wasn't too bad. After eating, he lay down on his bed and tried to get some sleep. Hopefully, he would have a few hours to dream about being elsewhere.

Rodney dreamt he was standing in the gate room and Elizabeth was standing in front of him. They walked towards each other and he drew her in to an embrace. Even as he was dreaming he knew that this wasn't real, but he felt safe and happy.


	5. Chapter 5

Part 5: Homecoming

Summary: A Ghost From the Past Returns to Atlantis.

It was the dead of night and Dr Rodney McKay was keeping a low profile as he crept silently around the wooden farm buildings. He dodged out from the shelter of the buildings to the cover of the long dry grass and than ran towards the Stargate as though his life depended upon it. At last he had the Stargate in sight and as he got closer and the gate loomed larger in his vision, the only thing he could think about was home. He reached the DHD and scanned the area for guards. The last thing he could afford was to be caught. Fortunately, there were few guards on the surface. The Genii relied on secrecy and armed guards around the gate would negate that.

The coast was clear and Rodney began dialling. He knew that this was the riskiest point of his escape and his hands shook with barely controlled fear as he pressed the final symbol. As soon as the gate sprang into life and the chevrons started to light up, an alarm went off. His trembling intensified as he heard soldiers in the distance. He knew that if he was caught, it would be the end, especially after what he had done just prior to his escaping.

Rodney was waiting for the chevrons to align as the guards closed in. They were yelling something but he wasn't paying attention to what, all he cared about was escaping. The last chevron locked into place and the Stargate opened with its familiar whoosh. Rodney ran to the gate as fast as his legs could carry him, jumped through and the gate shut down.

He arrived on a planet he knew to be uninhabited. He ran to the DHD and entered a new address as fast as he could. That way, on the remote chance that the soldiers had seen the gate address, they wouldn't be able to find him.

Rodney was desperate not to be caught and the tight knot of fear in his chest lessened once the outgoing wormhole had been established.

Rodney was now at the former Pegasus alpha site. His adrenaline rush was subsiding and he felt weak as he walked slowly to the DHD. He dialled Atlantis before he could even gather his thoughts not wanting to think about what was going to happen when he'd got home – when his friends had found out what he had done to save his pitiful skin. Once the gate had been dialled Rodney reached into his pocket, took out a small Genii field radio and checked the frequency.

Everyone on the Atlantis expedition hated the graveyard shift. The gate was kept manned to allow off-world teams to return if they needed and to guard against attacks. Usually it just involved babysitting the gate and trying to stay awake. Nobody in the gate room on duty that night realised that this shift would be different. The team monitoring the gate was surprised when the gate jumped to life. They immediately called in the unscheduled off-world activation and summoned Elizabeth.

A short time later Elizabeth ran into the control room. "We don't have any teams off-world, do we?" she asked.

"No," the technician replied, "but we are receiving a transmission and I don't think you'll believe it." The technician had a shocked look on his face.

"Let's hear it."

The technician tapped quickly on the controls in front of him to route the transmission through the main tannoy. Nobody in the control room could believe their ears when they heard the voice they never thought they would hear again speaking.

"This is Dr Rodney McKay, Atlantis, do you hear me?"

Elizabeth could barely believe it. It was Rodney, but he was dead and had been for over a year. She watched him die. Then she realised she only saw Kolya shoot Rodney, she hadn't seen Rodney actually die.

The thought that she'd abandoned him made Elizabeth feel physically sick. "Rodney! Rodney! Is that you?"

"Yes Elizabeth, it's me, lower the shield so I can get through," Rodney replied.

John Sheppard shook his head. "Elizabeth, as much as I want Rodney to be alive, we have to consider the possibility that this is a trap." There was something in John's eyes, something dark. It was the same thing she had seen when Kolya was holding her hostage. This was the side of John which knew what had to be done, the side nobody dared argue with.

Part of Elizabeth wanted to lower the shield and see Rodney step through the gate but at the same time, part of her agreed with John. This could be a trap and the Genii may be using this as an opportunity to invade Atlantis.

Elizabeth tapped her headset. "This is Dr Weir, I want security teams in the gate room," she said. She waited for the teams to arrive and nodded at John as he ran down the steps into the gate room to join the team of marines. She turned to the technician and ordered, "Lower the shield."

Struggling to maintain her calm facade Elizabeth stared steadfastly at the gate. She saw a dishevelled Rodney McKay step through the gate and when she saw him her composure deserted her and her eyes welled up with tears. She ran down the stairs and over to Rodney and threw herself into his arms hugging him fiercely. The days events finally took their toll as Rodney passed out, still in Elizabeth's arms.

Later, in the infirmary, Rodney was resting. Elizabeth walked in looking more resolute than she had in the gate room. She walked up to Carson. "How is he?" she asked.

Carson hesitated before answering, "Well he seems to be in good health. He's lost weight but he doesn't seem malnourished."

"Good." Elizabeth was starting to feel relieved.

"But he has a number of..." The doctor paused and looked sombre. "injuries," he continued

Elizabeth frowned. "What kind of injuries?"

"Well, for a start, the x-rays show a number of cracked ribs. They're healed, but they aren't in his records." Carson sighed. "Elizabeth, I think that it's safe to say that he's been beaten, badly. There's also significant scarring on his back which is consistent with a whip or similar implement. From the extent of his injuries, I'd say that he really pissed someone off."

"The last time I tried to escape," a weak voice interrupted. It was Rodney; he was awake and lying on his side looking away from Carson and Elizabeth.

Elizabeth walked over to Rodney and laid a hand on his shoulder and then quickly removed it as he flinched from her touch. "You tried to escape before? Is that why they did this to you?" she asked. It was growing increasingly difficult for Elizabeth to maintain her calm façade as the level of suffering he had gone through became clearer to her. She found it difficult to imagine what he had endured.

Rodney nodded.

Elizabeth's heart sank further. Tears were running down her face. She moved closer to him and kissed him on the cheek. She wanted to tell him how she felt, but with everything he'd been through she thought it better to wait. Her lips curved into a small smile. "Try to get some rest," she whispered and Rodney closed his eyes against the hot sting of tears. He hoped to fall in to a dreamless sleep but as it was he'd have no such luck.

The nightmares were about to start.


	6. Chapter 6

Part 6: The Truth Hurts

Summary: Rodney explains his ordeal to his friends.

He was standing in the gate room, Kolya had a gun to his head and was pulling him towards the gate. This time it was different, there was no security team and the room was empty, not even Elizabeth was there. He was alone and all he could hear were the menacing words from Kolya. "This time there is no escape."

He felt Kolya's gun pressing in to his spine, he could hear the trigger being drawn back. The sound of a gunshot echoed around the gate room, pulling him from the nightmare. He sat bolt upright to the ringing of his alarm clock. "It was a dream, it was just a dream," he muttered to himself though his words gave him scant reassurance.

When he'd arrived back on Atlantis, Rodney spent a few days in the infirmary while Carson made sure he was physically alright. After a few days he was going stir crazy and he thought it would be good to spend the night in his own quarters. He knew that today would be a long day - it was the day for his debriefing. He was dreading the meeting and what he would have to tell everyone.

Rodney didn't know what he dreaded more, explaining that he helped the Genii build missiles, or telling everyone about the way he'd been treated. Telling them exactly what happened.

The way he'd caved in.

Rodney was sitting in Elizabeth's office; John, Teyla, Ronon, Carson and Bates were also in attendance. Elizabeth opened the meeting by saying. "I know this must be difficult, but we just want to establish what happened while you were held captive," she said, her voice was as calm as ever.

"Well, I..." Rodney's voice trailed off. Elizabeth was worried because he wasn't making eye contact with her, he wasn't making eye contact with anyone.

"Dr McKay, did you provide the Genii with any advanced technology?" Bates asked in his usual abrupt manner.

"Don't you think you're being a little paranoid?" John asked.

"With all due respect, sir, we have to find out if Dr McKay provided the Genii with sensitive information."

Rodney's expression held none of the usual irritation which would usually follow from one of Sgt. Bates' stupid questions. The fact he was no longer speaking with his usual sarcasm made everyone worried about him.

Teyla laid a hand on Rodney's shoulder and said, "Dr McKay, we will not blame if the Genii forced you to help them."

Rodney still couldn't meet anyone's eye, he stared down at the table ashamed of what he was about to say. "I gave the Genii missile technology," he said in a broken whisper.

"What?" yelled Bates. "How could you give them that kind of technology?"

"That's enough!" Elizabeth shouted, her sudden outburst seemed to shock everyone.

"Relax, Bates, it's not like their missiles can be used against Atlantis," John said. "unless they manage to bypass the gate shield. In which case we're screwed anyway."

Rodney looked up, his face stricken. "I'm sorry. They wanted me to make C4. I told them that I couldn't, so they were going to kill me. I was scared, I was bargaining for my life and I told them about missile technology. It was the only thing I could think of."

Elizabeth's stomach twisted. She could see the pain and self loathing in Rodney's face. It saddened and angered her that this is what the Genii had reduced Rodney to. She laid a hand on his arm, to steady him, and said, "I understand, Rodney, and we'll need you to explain exactly how much help you gave the Genii and how advanced their missile program is. But there is something else I want to ask you about first. In the infirmary you told me about a previous escape attempt."

Rodney evaded her eye and looked back down. "It was about two or three months after I started working on the missile project. I used some components I stole from the lab to produce a makeshift GDO." Memories came flooding back as he described the events of that day...

His escape attempt started in the evening. He'd been working in the lab, when Kolya walked in. "Dr McKay, I'm impressed with your work. The Genii owe you a great debt of gratitude," he said, not that Rodney was paying much attention.

"Well, if you let me go, we'll call it even," retorted Rodney, as he left the room. He couldn't help but let out a small smile at the thought of his impending escape. The time was almost right, but as Rodney approached his quarters, his heart sank. A soldier was standing guard by the door, this was going to complicate matters. Although he seemed young and inexperienced, he looked formidable.

Later, Rodney was waiting to put his plan in to action. Over the past three months, Rodney had started to familiarise himself with the guards' patrols. He listened to when they were near his quarters. Until a month after he arrived, there'd been a permanent guard outside his quarters. By now they trusted him enough to remove that precaution and he couldn't understand why they'd decided to post a guard tonight of all nights. They were used to him going to his lab at all hours to, according to Rodney, to test new theories at odd hours. He had occasionally taken the opportunity to observe other patrol routes and familiarise himself with the complex. If he was seen, he told them that he was going to the lab to test some new idea. Fortunately that had only happened a few times, so none of the guards became suspicious. Now he thought he had enough information.

The opening of his door was met by the suspicious gaze of the young Genii soldier. "What? Can't I go to my own lab?" he blustered.

"I'm to escort you to and from the facilities," he replied. This didn't seem good, was there a chance they suspected what he was up to?

"Okay then, but I need to get to the commissary first. What's the fastest route?"

As the guard was distracted pointing to a junction, Rodney reached back to a metal rod he had tucked in to his waistband. Before the guard had finished with the directions, Rodney swung the heavy rod and hit him square on the back of his head. As the guard fell Rodney instinctively grabbed him, trying not to think about the sickening thud. After dragging him in to his quarters, he checked the soldier's pulse. Relieved that the soldier, who seemed little more than a kid, was alive, Rodney grabbed his gun and tucked it in to the waistband which had held his last weapon. Then, with some trepidation, he started his journey to the surface.

Once on the surface, he checked for signs of guards. So far, so good. He was about to start his run to the gate when he noticed the stars and for a few moments he soaked in the beauty of the night sky he hadn't seen for so long. It was a pleasant distraction from the worry of finding the gate. "You only found this place by chance, and that was during the day!" he thought to himself. Rodney felt tense, afraid of being found but although terrified, he still enjoyed the adrenaline rush. It was part of the reason worked in the field with Sheppard. Soon, he saw the gate, he was almost home.

He started dialling the address for Atlantis into the DHD and the Chevrons lit up with a hum, each one sounding like a call to home. Once the wormhole was established, he took out the field radio he'd stolen a month ago.

"This is going to work, I'm going to get out of here," he repeated like a mantra. It was all Rodney could think about as he fumbled with the settings. He was so intent on his work, he didn't notice Kolya growing ever closer. He was nearly at the event horizon when Kolya grabbed him.

"No!" yelled Rodney and struggled with all his might, but it was no use against the more powerful man. He wasn't going anywhere.

"Going somewhere, Dr McKay?" asked the Genii commander, in a deep and threatening voice.

Rodney continued to struggle. "You bastard! Let me go!" His thrashing started to slow as his strength was drained, along with his hopes.

"I'm sorry Dr McKay, you know I can't do that." The mock sincerity in Kolya's voice was enough to terrify Rodney into stillness.

"Please, let me go," He knew he sounded desperate, he was.

A troop of Genii soldiers had now surrounded Rodney and Kolya, their rifles trained on Rodney. Most Genii already hated him, after all, Sheppard killed nearly 60 of them when they tried to take Atlantis. One of them stepped forward and grabbed his arms, tying them behind his back.

Rodney watched the wormhole close, taking his last hopes of escape with it.

"You disappoint me, Dr McKay," Kolya said as he marched Rodney back to the complex. "Do you remember what I told you when you first arrived?"

"I was drugged and recovering from surgery after you'd shot me, do you seriously expect me to remember every threat you uttered?" Rodney was starting to sound a little more like his usual sarcastic self, although his insides were turning to water.

Kolya shook his head, his features grim. "I told you that you would be punished if you tried to escape. You earned our trust and now you have betrayed us."

Rodney was led back in to the underground complex and to Cowen's office. To say that Cowen looked angry would have been an understatement.

Cowen counted up on his fingers as he read out charges. "Attempted escape, theft, assault. Do you have anything to say for yourself?"

Rodney looked drained, though he still managed a small spark of defiance. "The first duty of a prisoner is to escape."


	7. Chapter 7

Chapter 7: This can't possibly get any worse

Summary: His escape attempt thwarted, Rodney learns the hard way just how ruthless the Genii can be.

Atlantis

The tense silence was broken by Sheppard. "You're tougher than I gave you credit for," said the major with a wry twist to his mouth.

"Thanks," Rodney replied, "I guess working with you has its advantages." Elizabeth smiled, she found it reassuring that some of the scientist's acerbic wit was starting to return. Her countenance became more serious as she considered how to phrase her next question. "Rodney, you know that Carson told me that there were signs that you'd been," it took a moment to find the right words, "mistreated by the Genii?"

He nodded.

"Can you tell us what happened?"

She could see the pain in his eyes as she asked the question.

Here was the moment Rodney had been dreading. Shame filled him as he remembered the terrible details. "They tried to," he stopped and then took a deep breath before continuing, "to persuade me that it wasn't in my best interests to attempt escape."

The Genii Home World

"Commander Kolya," Kolya stood to attention at Cowen's words, "I want you to ensure that Dr McKay understands the consequences of his actions." As Kolya nodded, Rodney felt the knot in his stomach tighten. What did this maniac have planned? He didn't have particularly fond memories of the "quality time" he'd spent with Kolya when he'd tried to take Atlantis from them. He still cringed at the thought of Kolya's knife being twisted in his arm; the way Kolya had broken him.

Two guards pulled Rodney from his chair and out of the room. Sick with fear he stumbled along between them barely registering where he was going.

Rodney landed hard in, what looked to be, a featureless room. The single flickering bulb, the only source of light in this depressing hole, added to his unease. As he started to draw himself up, he noticed that one of the guards seemed familiar. He stared at Rodney, his eyes filled with malice as he snarled, "The man you attacked was Goran, my brother. I don't know if he's going to wake up again, you bastard."

The blow to Rodney's stomach caught him off guard and he fell heavily to his knees. Then, for what felt like an eternity the distraught soldier took his revenge in a frenzy of kicking and punching that left Rodney with no choice but the curl into a ball on the floor in a futile attempt to reduce the damage. As he lay there taking the punishment that was being meted out to him, Rodney thought back to his concern for the young soldier's safety, trying to cling the shred of humanity that separated him from his captors.

Kolya entered the room and dispassionately studied the scene before him. "All right that's enough," he said and the guards ceased their onslaught. "We don't want to risk permanently damaging McKay. He has work to do," he said.

In that moment Rodney's hopes soared. The lesson was over. Rodney was pulled to his feet, dazed and sore from the battering. He felt a sharp pain along his right side and although he didn't know much about Carson's voodoo he knew enough to know that he had a few cracked ribs.

Kolya looked over to a post at the end of the room. "Remove his shirt," he said in a matter of fact voice, "then prepare him."

"What?" Rodney asked weakly, shaking his head. "I don't understand, what's going on?"

Kolya shook his head. "Did you honestly think that was it?" he asked. "We trusted you and in return you betrayed us, now you must learn the consequences of those actions."

"Betrayed? Trust? You shot me and then kidnapped me, what did you think I'd do, say thanks for taking me away from everything and everyone I know?" Rodney knew he was digging himself a bigger hole, but he was past caring.

"Dr McKay, I know that you have a sentimental attachment to your uniform, so I'm giving you the chance to avoid having it damaged." Kolya was reaching for his knife as Rodney got the message. This wasn't going to end well.

"No!" Rodney yelled. "No! You people are nuts! Your whole society's screwed up!" By now he was waving his arms around as though he was in a heated debate with Radek. "This whole thing about trust and betrayal is just some sick mind control game, Kolya!" his rant was cut short as the guards grabbed him again. The realisation of his situation was slowly starting to set in, there was no reasoning with these people."

Kolya waited a moment until he was sure the ever irritating Rodney McKay had calmed down before starting to draw his knife. "Well? Do I need to slice it off you?"

The colour drained from Rodney's face, "No, that won't be necessary," he replied. Kolya nodded to the guards, signalling them to release him. Rodney could barely believe that this was happening, everything had spiralled out of control. While trying to regain his composure, he slowly peeled off his jacket and let it fall to the ground. With a growing sense of dread he took off his shirt and dropped it by his jacket. Seeing the bullet hole in his shirt he was reminded of why he had tried to escape, why he had to escape. For a moment he considered trying to make a run for it, but there was no point. They'd catch him before he made it to the door and his punishment would probably be much worse. There was nothing more he could do.

Kolya nodded to the guards. Rodney stood straight, the one thing the Genii hadn't taken was his dignity.

The soldiers pulled him over to the post and he went with them, powerless, impotent, and resigned to his fate. In short order Rodney found his wrists bound to the post, above his head. The actual realisation of what was about to happen started to set in. He began to tremble, praying to a god he didn't believe in. He heard the sound of the whip cracking. All Rodney could think about was that he had never been closer to home, and never been further away from it at the same time, as he had been earlier.

I'm sorry that this has to happen, Dr McKay," Kolya said softly to him, sounding sympathetic. Then his demeanour changed and he began to speak in a more formal tone, addressing the room rather than the scientist.

"The charges levelled against you are theft, assault and desertion. On the charge of theft, you are found guilty. On the charge of assault, you are found guilty. On the charge of desertion, you are found guilty . Do you have anything to say before sentence is carried out?"

"It wasn't desertion, I was just trying to get home."

Kolya ignored him and continued, "The sentence is fifty lashes. Do you wish to plead for clemency?"

I'm not going to give this bastard the satisfaction of hearing me beg. "Just get this over with," Rodney replied dully and in that moment, he remembered his mantra in full, the first duty of a prisoner is to survive, the second is to escape.

"Very well." Kolya nodded to the soldier to whom he had handed the whip. Rodney closed his eyes and tried to prepare himself for the worst.

It wasn't until the third blow that he cried out.

Atlantis

There was a tense silence, everyone had clearly been shocked by Rodney's revelation. Teyla reached over again and held Rodney's hand. "Dr McKay, I am sorry for what has happened to you. We all are."

Rodney managed a weak smile, it didn't last long. He continued quietly, "I can't actually remember all of it. I.. I… must have blacked out, fortunately." He had a pained look in his eyes.

John started to speak, "I'm sorry, this is all my fault." He was shaking his head as if to deny what had happened to his friend. There was now a look of anger in his eyes. "I should have killed the bastard when I had the chance."

"It wasn't your fault, Sheppard so forget the martyr complex. You thought I was dead and I understand. Anyway, it didn't work. It just made me want to get away even more. So after I recovered I started planning how I was going to escape. That's all I want to say about it." Rodney took in a deep breath.

"Just before I escaped, I planted a little surprise in the computers they use for their calculations."

Johns eyebrows rose in surprise. "Dare I ask?"

"The modifications I made were designed to activate if I didn't enter an abort code. That way if I was killed or managed to escape it would start, leaving me safe if I was brought back. It should have activated a few hours ago, all the data their computers now produce will be garbage. It should also be printing snide remarks about Cowen and a few other surprises. I was being creative at the time, should take them a while to fix.

John grinned and then said, "Rodney McKay, the master hacker."

"So with any luck it could be months or even years before they get their research program back on track?" Bates interjected. Rodney nodded, not paying much attention.

He started to drift as he remembered the meticulous planning that went in to the sabotage. This was his revenge for what they'd done to him. From disguising the malicious subroutines to placing the dead man's switch that would set it off after a few days, he knew he could make life much more difficult for the Genii scientists after he'd left. He only wished he could see the look on Cowen's face as their flagship project crumbled around him. Then again, he hoped never to see the bastard's face again.

The rest of the meeting was a blur. Rodney found it strange: he almost felt like he wasn't there, like he didn't connect with this place or these people. Afterwards, he returned to his quarters. Like everything that day, the room didn't feel right. It was no longer his sanctuary from stresses of daily life.

Rodney had hoped that things would return to normal once he'd told his team what had happened but this was not the case. He felt hollow, it almost seemed like he'd left part of himself in the Genii underground complex.

He hated them for that and he hated himself for helping them.


End file.
